Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
Open Access
- 22 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 22 (1), 1-21
- https://doi.org/10.1186/s13059-021-02283-5
Abstract
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no complete software for detecting SNPs, phasing haplotypes, and mapping methylation to these from nanopore sequence data. Here, we present NanoMethPhase, a software tool to phase 5-methylcytosine from nanopore sequencing. We also present SNVoter, which can post-process nanopore SNV calls to improve accuracy in low coverage regions. Together, these tools can accurately detect allele-specific methylation genome-wide using nanopore sequence data with low coverage of about ten-fold redundancy.Funding Information
- The University of British Columbia Four Year Doctoral Fellowship
- Canada Research Chairs
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